Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this
to extract flanking regions for cloning. If the result of the multiple sequence alignment is
not as expected, these results could be used for further investigation.
qseqid
sseqid
percentage.identical
alignment.length
no.mismatch
no.gap.openings
qstart
qend
sstart
send
evalue
bitscore
0
TraesCS2A01G106300
chr2A
100.000
2661
0
0
1
2661
58507143
58504483
0
4915
1
TraesCS2A01G106300
chr2A
96.761
1914
55
6
1
1909
733073864
733075775
0
3184
2
TraesCS2A01G106300
chr2A
99.468
752
2
2
1910
2661
58498190
58497441
0
1365
3
TraesCS2A01G106300
chr2A
98.283
757
9
4
1907
2661
85673754
85674508
0
1323
4
TraesCS2A01G106300
chr7A
96.970
1914
51
6
1
1909
722692713
722690802
0
3206
5
TraesCS2A01G106300
chr6A
96.862
1912
52
7
1
1909
554918368
554920274
0
3192
6
TraesCS2A01G106300
chr6A
98.406
753
9
3
1910
2661
584791405
584792155
0
1321
7
TraesCS2A01G106300
chr5A
96.815
1915
54
6
1
1909
624937748
624935835
0
3192
8
TraesCS2A01G106300
chr4A
96.813
1914
55
5
1
1909
592482780
592484692
0
3192
9
TraesCS2A01G106300
chr4A
96.813
1914
55
5
1
1909
592761586
592763498
0
3192
10
TraesCS2A01G106300
chr4A
96.708
1914
57
5
1
1909
593049664
593051576
0
3181
11
TraesCS2A01G106300
chr4A
98.541
754
7
4
1907
2658
349724217
349724968
0
1328
12
TraesCS2A01G106300
chr1A
96.813
1914
53
7
1
1909
21070270
21068360
0
3190
13
TraesCS2A01G106300
chr3A
96.761
1914
55
6
1
1909
42788380
42786469
0
3184
14
TraesCS2A01G106300
chr7B
98.539
753
8
3
1910
2661
440859315
440860065
0
1327
15
TraesCS2A01G106300
chr6B
98.539
753
8
3
1910
2661
351838087
351837337
0
1327
16
TraesCS2A01G106300
chr6B
98.039
765
10
5
1899
2661
351856282
351855521
0
1325
17
TraesCS2A01G106300
chr6B
98.406
753
9
3
1910
2661
522913122
522913872
0
1321
18
TraesCS2A01G106300
chr5B
98.406
753
8
4
1910
2661
696913899
696914648
0
1321
These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the
BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are
purely upstream or downstream may be removed if they don't overlap both primers.
query
scaffold
start
end
length
rev.comp
avg.bitscore
max.bitscore
avg.percent.identical
query.start
query.end
num_hsp
groupid
homo_length
0
TraesCS2A01G106300
chr2A
58504483
58507143
2660
True
4915
4915
100.000
1
2661
1
chr2A.!!$R2
2660
1
TraesCS2A01G106300
chr2A
733073864
733075775
1911
False
3184
3184
96.761
1
1909
1
chr2A.!!$F2
1908
2
TraesCS2A01G106300
chr2A
58497441
58498190
749
True
1365
1365
99.468
1910
2661
1
chr2A.!!$R1
751
3
TraesCS2A01G106300
chr2A
85673754
85674508
754
False
1323
1323
98.283
1907
2661
1
chr2A.!!$F1
754
4
TraesCS2A01G106300
chr7A
722690802
722692713
1911
True
3206
3206
96.970
1
1909
1
chr7A.!!$R1
1908
5
TraesCS2A01G106300
chr6A
554918368
554920274
1906
False
3192
3192
96.862
1
1909
1
chr6A.!!$F1
1908
6
TraesCS2A01G106300
chr6A
584791405
584792155
750
False
1321
1321
98.406
1910
2661
1
chr6A.!!$F2
751
7
TraesCS2A01G106300
chr5A
624935835
624937748
1913
True
3192
3192
96.815
1
1909
1
chr5A.!!$R1
1908
8
TraesCS2A01G106300
chr4A
592482780
592484692
1912
False
3192
3192
96.813
1
1909
1
chr4A.!!$F2
1908
9
TraesCS2A01G106300
chr4A
592761586
592763498
1912
False
3192
3192
96.813
1
1909
1
chr4A.!!$F3
1908
10
TraesCS2A01G106300
chr4A
593049664
593051576
1912
False
3181
3181
96.708
1
1909
1
chr4A.!!$F4
1908
11
TraesCS2A01G106300
chr4A
349724217
349724968
751
False
1328
1328
98.541
1907
2658
1
chr4A.!!$F1
751
12
TraesCS2A01G106300
chr1A
21068360
21070270
1910
True
3190
3190
96.813
1
1909
1
chr1A.!!$R1
1908
13
TraesCS2A01G106300
chr3A
42786469
42788380
1911
True
3184
3184
96.761
1
1909
1
chr3A.!!$R1
1908
14
TraesCS2A01G106300
chr7B
440859315
440860065
750
False
1327
1327
98.539
1910
2661
1
chr7B.!!$F1
751
15
TraesCS2A01G106300
chr6B
351837337
351838087
750
True
1327
1327
98.539
1910
2661
1
chr6B.!!$R1
751
16
TraesCS2A01G106300
chr6B
351855521
351856282
761
True
1325
1325
98.039
1899
2661
1
chr6B.!!$R2
762
17
TraesCS2A01G106300
chr6B
522913122
522913872
750
False
1321
1321
98.406
1910
2661
1
chr6B.!!$F1
751
18
TraesCS2A01G106300
chr5B
696913899
696914648
749
False
1321
1321
98.406
1910
2661
1
chr5B.!!$F1
751
AutoCloner calculated primer pairs
These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3),
whilst remaining within the specified product range where possible.
Listed here are all possible primers based on the multiple sequence alignment and SNPs generated
previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work
during PCR or sequencing,
these could be used as alternatives.